[phenixbb] Geometry Restraints - UPDATE

Edward A. Berry BerryE at upstate.edu
Wed Apr 25 06:36:10 PDT 2012

1. If you take the final refined structure and refine against the
original anisotropic data, does the geometry go bad again? It would
be interesting to know if fixing the anisotropy fixed the problem, or
fixing the anisotropy improved the maps so you could see the problem
and fix it in coot.

2. When you deposit the structure in the PDB, will you supply the
anisotropy-corrected data, or the original raw data?


Mario Sanches wrote:
> Last week I asked a question about geometry restraints at low
> resolution. I would like to thank you all that took the time to answer,
> specially Pavel for looking at the data. First, here is the original
> question:
> __________________________________________
> I am refining a low resolution structure (2.9A) using phenix.refine. As
> I continue the refinement  Rwork/Rfree are dropping but my  geometry
> statistics in general are very bad. My clashscore is getting worst and
> the RMS(angle) is really high. I have tried to play with the "wxc_scale"
>   parameter and also ran phenix selecting the "Optimize X-ray/ADP
> weight" option. All attempts end with a RMS(angle) of ~3.8 and a
> Clashscore of ~190.
> Is there a known procedure to deal with this? I feel that my geometry
> weighing term is too loose but I don't know exactly how to tighten it
> other than decreasing the wxc_scale parameter. I have gone and manually
> corrected bad positions before but given the low resolution nature of
> the structure the clashes tend to be reestablished during refinement.
> Thank you in advance for your help,
> __________________________________________
> It turns out that the reason to my nightmares was a highly anisotropic
> dataset. When I tried to fix geometry related problems in coot,
> phenix.refine was twisting the geometry back again, probably because it
> was trying to fit a lot of noise due to the anisotropy. Everything was
> getting worst, geometry, clashscore, and Ramachandran.
> Pavel finally corrected it by using this server:
> http://services.mbi.ucla.edu/anisoscale/  I should have been more
> diligent regarding that, since I could clearly see that my data was
> anisotropic from the diffraction images. I just didn't know how
> important this parameter could be. Anyways, phenix.xtriage will tell you
> if your data is anisotropic. The lesson is to pay attention to it.
> In my case, the quality of the electron density improved considerably,
> the geometry improved massively (manual intervention in coot was
> absolutely necessary, but now it stays correct after I manually fix the
> problems), clashscore lowered, etc.
> As a side note, it worked better without hydrogens in my case than with.
> It is certainly a parameter to try if you are having problems.
> Thank you all again for the tips.
> Mario Sanches
> --
> Mario Sanches
> Postdoctoral Researcher
> Samuel Lunenfeld Research Institute
> Mount Sinai Hospital
> 600 University Ave
> Toronto - Ontario
> Canada
> M5G 1X5
> http://ca.linkedin.com/in/mariosanches
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